Two months ago, we launched Gencove Consumer, a direct-to-consumer DNA test that uses low-pass whole genome sequencing to provide PRS results, ancestry, and access to raw data.
A few weeks later, we released developer access for Gencove Consumer, including a REST API, MCP server, and OAuth 2.0 flows for partner applications.
Today, we are adding another layer: variant-level API access.
The goal is simple. Gencove users and partners should be able to query specific genetic variants directly from a sample’s imputed VCF, without downloading and parsing a large VCF file themselves.
This matters because PRS and ancestry are only part of the consumer genetics story. They are important, useful starting points, but many products and users eventually ask more specific questions:
- What is the user’s genotype at a specific APOE-related variant?
- Can we look up a known MTHFR variant?
- Can a fitness or nutrition product retrieve variants such as ACTN3 or LCT?
- Can a partner query a small set of variants relevant to its own experience, without asking Gencove to predefine every possible result in advance?
These are the kinds of questions that come up when genetics becomes part of a broader consumer health product.
Why variant-level access matters
Consumer health products are becoming more data-rich. Many products already combine labs, wearables, imaging, family history, coaching, symptoms, lifestyle data, and longitudinal tracking.
Genetics is a natural additional layer, but it is not always useful in only one format.
For some use cases, a polygenic risk score is the right abstraction. PRS can combine information across many variants to estimate genetic predisposition for a condition or trait. For other use cases, partners may need to inspect one variant, a small set of variants, or a short genomic region.
That need is difficult to fully predict in advance.
One partner may be interested in pharmacogenomic markers. Another may be focused on fitness or nutrition. Another may want to explore well-known variants that are commonly discussed in consumer genetics, such as APOE, MTHFR, ACTN3, or LCT. New research also continues to appear, which means the set of variants people care about will keep changing over time.
Historically, the fallback has been raw data access: download the imputed VCF, parse it locally, and extract the relevant records.
That works for technical users, but it is not a great product integration pattern: VCFs can be large, they require domain-specific tooling, and they introduce additional storage, security, parsing, and operational complexity. Most consumer health companies do not want to build and maintain that layer just to answer a handful of variant-level questions.
Variant-level API access is meant to make this simpler.
Instead of moving the whole file around, a partner can ask Gencove for the variants it needs.
What we released
Gencove now supports variant-level access for both enterprise and consumer use cases.
For enterprise partners and their users, variant queries are available through the Gencove API:
GET https://api.gencove.com/api/v2/sample-genomic-variants/{sample_id}For Gencove Consumer users and partner applications acting on behalf of a consumer, variant queries are available through the Consumer API:
GET https://consumer.gencove.com/api/v1/kit-genomic-variants/{sample_id}/The endpoint reads from the sample’s imputed VCF and returns matching variant records as JSON. The query is made against a sample_id, which is available from the existing sample and kit endpoints.
A request must use exactly one of three query modes.
Point query
Use a point query when you know the exact chromosome and position.
curl "https://api.gencove.com/api/v2/sample-genomic-variants/$SAMPLE_ID?chromosome=chr19&position=44908684" \
-H "Authorization: Api-Key $GENCOVE_API_KEY"The consumer version uses the same query pattern:
curl "https://consumer.gencove.com/api/v1/kit-genomic-variants/$SAMPLE_ID/?chromosome=chr19&position=44908684" \
-H "Authorization: Api-Key $GENCOVE_CONSUMER_API_KEY"Point queries are useful when a product already knows the genomic coordinate it wants to inspect.
Range query
Use a range query when you want to retrieve all matching variants in a short genomic window.
curl "https://api.gencove.com/api/v2/sample-genomic-variants/$SAMPLE_ID?chromosome=chr11&start_position=5225464&end_position=5227000" \
-H "Authorization: Api-Key $GENCOVE_API_KEY"And for consumer:
curl "https://consumer.gencove.com/api/v1/kit-genomic-variants/$SAMPLE_ID/?chromosome=chr11&start_position=5225464&end_position=5227000" \
-H "Authorization: Api-Key $GENCOVE_CONSUMER_API_KEY"Range queries are useful when an application wants to inspect a bounded region rather than a single coordinate. Ranges are intentionally capped so the API remains focused on targeted access rather than bulk VCF export.
rsID query
Use an rsID query when you want to retrieve one or more variants by dbSNP identifier.
curl "https://api.gencove.com/api/v2/sample-genomic-variants/$SAMPLE_ID?rsid=rs429358,rs7412,rs1801133,rs1815739,rs4988235" \
-H "Authorization: Api-Key $GENCOVE_API_KEY"And for consumer:
curl "https://consumer.gencove.com/api/v1/kit-genomic-variants/$SAMPLE_ID/?rsid=rs429358,rs7412,rs1801133,rs1815739,rs4988235" \
-H "Authorization: Api-Key $GENCOVE_CONSUMER_API_KEY"This example includes commonly discussed variants associated with APOE, MTHFR, ACTN3, and LCT. The API resolves supported rsIDs to genomic coordinates and returns the matching records from the sample’s imputed VCF.
The important point is that partner products can request the variants relevant to their own experience, without needing to download the full VCF or wait for Gencove to create a bespoke report for every possible use case.
What the response looks like
Variant-level responses are returned as JSON. A response includes the chromosome, position, rsID when available, reference and alternate alleles, genotype fields, and related VCF information.
For example:
{
"count": 1,
"next_offset": null,
"results": [
{
"chromosome": "chr19",
"position": 44908684,
"rsid": "rs429358",
"ref": "T",
"alt": ["C"],
"genotype": {
"GT": "0|1",
"DS": "1",
"GP": "0,1,0"
},
"quality": null,
"info": {
"RAF": "0.15"
}
}
]
}The exact interpretation of a variant depends on the product context, scientific evidence, population context, and any applicable clinical or regulatory considerations. The API provides structured access to the underlying variant data; it does not turn every variant into a medical interpretation by itself.
That separation is intentional. Some partners want raw variant access because they already have their own scientific model, report logic, or product experience. Others may use variant access as one input alongside PRS, ancestry, labs, family history, or wearable data.
Consumer access, partner access, and MCP
For individual users and developers, personal API keys provide the fastest way to query their own data.
For partner applications, OAuth is the right integration path. A partner application can request scoped access, the user can review and approve that request, and the partner can call the API using a bearer token. For variant-level access, partner applications request the genomic_variants:read scope.
Consumer users can also access this through the Gencove MCP server using the get_genomic_variants tool. This makes variant-level access available from AI tools and developer environments that support MCP.
That means a user could connect their Gencove account to an AI assistant and ask questions such as:
- “What is my genotype at rs429358?”
- “Show me the variants on chr11 between these positions.”
- “Do I carry the APOE-related variants rs429358 and rs7412?”
The assistant can then call the MCP tool and answer using the user’s real Gencove data, rather than relying on a manually uploaded VCF or copied snippets from a report.
What partners can build
Variant-level access is most useful when genetics is one layer inside a broader product.
A preventive health product may combine PRS, selected variants, labs, age, sex, family history, and screening guidelines.
A longevity product may want genetics to sit alongside biomarkers, imaging, wearable signals, interventions, and longitudinal tracking.
A fitness or nutrition product may want to inspect a small number of variants related to its own experience, while still treating genetics as one input among training history, sleep, recovery, diet, and goals.
A pharmacogenomics or medication-safety workflow may want to retrieve specific markers relevant to its own evidence base and interpretation logic.
In each case, the value is not that genetics becomes the whole product. The value is that genetics can be integrated into products where it adds useful context.
That is the broader direction for Gencove Consumer and the Gencove platform: make genetic data easier to access, easier to connect, and easier to build on, without requiring every company to become a sequencing, bioinformatics, and genomic infrastructure company.
Built for targeted access
Variant-level API access is designed for targeted queries, not bulk data export.
For bulk access, the raw VCF remains available. For product integrations that need a handful of variants, a short coordinate range, or a list of rsIDs, the API provides a cleaner path.
This gives partners a practical middle ground:
- PRS and ancestry for higher-level genetic results
- raw data files when full data access is needed
- variant-level API access when an application needs specific records from the imputed VCF
That combination is important because consumer genetics products do not all need the same abstraction. Some need reports. Some need files. Some need a specific variant. Many will need all three at different points in the user experience.
Getting started
Enterprise customers can read the variant-level API documentation in the Gencove Enterprise docs. The enterprise endpoint is:
GET https://api.gencove.com/api/v2/sample-genomic-variants/{sample_id}Developers working with Gencove Consumer can start with the Consumer developer documentation. The consumer endpoint is:
GET https://consumer.gencove.com/api/v1/kit-genomic-variants/{sample_id}/The same data is also available through the Gencove MCP server using the get_genomic_variants tool.
For companies building in preventive care, fitness, nutrition, longevity, pharmacogenomics, or adjacent consumer health categories, we would be interested in discussing how Gencove can help bring genetics into your product.
Two months ago, Gencove Consumer made it easier for individuals to access PRS, ancestry, and raw genetic data through a low-pass sequencing-based test. With API, OAuth, MCP, and now variant-level access, that data can be used more directly in the products and tools consumers choose to connect.